chr1-42959040-CT-C

Position:

• chr1-42959040-CT-C

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_Strong BA1

The variant allele was found at a frequency of 0.218 in 220,588 control chromosomes in the GnomAD database, including 5,620 homozygotes. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.23 (4176 hom., cov: 26)
  • Exomes 𝑓: 0.19 (1444 hom.)
• Consequence: intergenic_region
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:8
• Conservation: PhyloP100: 0.718

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -16 ACMG points.

• BP6: Variant 1-42959040-CT-C is Benign according to our data. Variant chr1-42959040-CT-C is described in ClinVar as [Benign]. Clinvar id is 297392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.42959041delT		intergenic_region
SLC2A1-DT	NR_033967.1	n.-8delT		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A1-DT	ENST00000416689.2	n.-32delT		upstream_gene_variant		2
SLC2A1-DT	ENST00000431759.6	n.-8delT		upstream_gene_variant		2
SLC2A1-DT	ENST00000653200.1	n.-37delT		upstream_gene_variant
ENSG00000283973	ENST00000640236.1	n.*24delA		downstream_gene_variant		4

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35091 AN: 151988 Hom.: 4175 Cov.: 26

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.223

GnomAD4 exome AF: 0.190 AC: 13033 AN: 68482 Hom.: 1444 Cov.: 0 AF XY: 0.191 AC XY: 7055 AN XY: 36914

Gnomad4 AFR exome AF: 0.227

Gnomad4 AMR exome AF: 0.204

Gnomad4 ASJ exome AF: 0.195

Gnomad4 EAS exome AF: 0.180

Gnomad4 SAS exome AF: 0.202

Gnomad4 FIN exome AF: 0.208

Gnomad4 NFE exome AF: 0.185

Gnomad4 OTH exome AF: 0.191

GnomAD4 genome AF: 0.231 AC: 35119 AN: 152106 Hom.: 4176 Cov.: 26 AF XY: 0.234 AC XY: 17403 AN XY: 74350

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.228

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.225

Alfa AF: 0.0646 Hom.: 138

Bravo AF: 0.230

Asia WGS AF: 0.243 AC: 845 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:8

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Dystonia 9 Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Apr 11, 2023

- -

Encephalopathy due to GLUT1 deficiency Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Apr 11, 2023

- -

Childhood onset GLUT1 deficiency syndrome 2 Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Apr 11, 2023

- -

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 18, 2018

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

GLUT1 deficiency syndrome Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Dystonic disorder Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Hereditary cryohydrocytosis with reduced stomatin Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Apr 11, 2023

- -

Epilepsy, idiopathic generalized, susceptibility to, 12 Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Apr 11, 2023

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs28365848; hg19: chr1-43424711;